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authorLars-Dominik Braun <lars@6xq.net>2021-10-05 15:42:38 +0200
committerLars-Dominik Braun <lars@6xq.net>2021-10-08 09:13:54 +0200
commitfb1ffc53ba6177e28aa296ae2e9c2e812f92e28e (patch)
tree86674f7b7fb0b8fa628d73c648b535ab174ca94c /gnu/packages
parentff5fea3dfe64b933f7698134de9dba14ef8d0694 (diff)
gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm10
-rw-r--r--gnu/packages/patches/pigx-bsseq-no-citeproc.patch33
2 files changed, 41 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 932073ef5a..63e91438cb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10644,7 +10644,8 @@ in an easily configurable manner.")
"/pigx_bsseq-" version ".tar.gz"))
(sha256
(base32
- "05al5dacfp1vf1x3cq20jhd6w4xj5vaxslzaka6yrpg0av8sh3k3"))))
+ "05al5dacfp1vf1x3cq20jhd6w4xj5vaxslzaka6yrpg0av8sh3k3"))
+ (patches (search-patches "pigx-bsseq-no-citeproc.patch"))))
(build-system gnu-build-system)
(arguments
`(;; TODO: tests currently require 12+GB of RAM. See
@@ -10652,6 +10653,9 @@ in an easily configurable manner.")
#:tests? #f
#:phases
(modify-phases %standard-phases
+ (add-before 'bootstrap 'autoreconf
+ (lambda _
+ (invoke "autoreconf" "-vif")))
(add-before 'check 'set-timezone
;; The readr package is picky about timezones.
(lambda* (#:key inputs #:allow-other-keys)
@@ -10660,7 +10664,9 @@ in an easily configurable manner.")
(string-append (assoc-ref inputs "tzdata")
"/share/zoneinfo")))))))
(native-inputs
- `(("tzdata" ,tzdata)))
+ `(("tzdata" ,tzdata)
+ ("automake" ,automake)
+ ("autoconf" ,autoconf)))
(inputs
`(("coreutils" ,coreutils)
("sed" ,sed)
diff --git a/gnu/packages/patches/pigx-bsseq-no-citeproc.patch b/gnu/packages/patches/pigx-bsseq-no-citeproc.patch
new file mode 100644
index 0000000000..882e660fe4
--- /dev/null
+++ b/gnu/packages/patches/pigx-bsseq-no-citeproc.patch
@@ -0,0 +1,33 @@
+diff -Naur pigx_bsseq-0.1.5/configure.ac pigx_bsseq-0.1.5.patched/configure.ac
+--- pigx_bsseq-0.1.5/configure.ac 2021-06-08 15:28:08.000000000 +0200
++++ pigx_bsseq-0.1.5.patched/configure.ac 2021-10-05 14:43:56.806529137 +0200
+@@ -38,7 +38,6 @@
+ find_or_override_prog([GNUBASH], [bash])
+ find_or_override_prog([SNAKEMAKE], [snakemake])
+ find_or_override_prog([PANDOC], [pandoc])
+-find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
+ find_or_override_prog([FASTQC], [fastqc])
+ find_or_override_prog([MULTIQC], [multiqc])
+ find_or_override_prog([TRIMGALORE], [trim_galore])
+diff -Naur pigx_bsseq-0.1.5/Makefile.in pigx_bsseq-0.1.5.patched/Makefile.in
+--- pigx_bsseq-0.1.5/Makefile.in 2021-06-08 16:17:03.000000000 +0200
++++ pigx_bsseq-0.1.5.patched/Makefile.in 2021-10-05 14:43:34.635876855 +0200
+@@ -408,7 +408,6 @@
+ PACKAGE_URL = @PACKAGE_URL@
+ PACKAGE_VERSION = @PACKAGE_VERSION@
+ PANDOC = @PANDOC@
+-PANDOC_CITEPROC = @PANDOC_CITEPROC@
+ PATH_SEPARATOR = @PATH_SEPARATOR@
+ PYTHON = @PYTHON@
+ PYTHONPATH = @PYTHONPATH@
+diff -Naur pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in
+--- pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in 2021-06-08 10:14:29.000000000 +0200
++++ pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in 2021-10-05 14:43:44.296161069 +0200
+@@ -375,7 +375,6 @@
+ if path.exists(bin): shutil.rmtree(bin)
+ os.makedirs(bin, exist_ok=True)
+ os.symlink('@PANDOC@', path.join(bin, "pandoc"))
+- os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc"))
+ os.symlink('@RSCRIPT@', path.join(bin, "Rscript"))
+ os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH']
+ os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH']